Files in venelin/PCMBase

Simulation and Likelihood Calculation of Phylogenetic Comparative Models

.Rbuildignore

.gitattributes

.gitignore

.travis.yml

DESCRIPTION

NAMESPACE

NEWS.md

PCMBase.Rproj

R/AutoGeneratedModelTypes.R R/BM.R R/BMdrift.R R/DOU.R R/DefaultModelTypes.R R/GaussianPCM.R R/JOU.R R/LatexTools.R R/MixedGaussian.R R/OU.R R/PCM.R R/PCMBaseTestObjects.R R/PCMParam.R R/PCMTable.R R/PCMTree.R R/Utilities.R R/White.R R/matrixparametrizations.R R/zzz.R README.Rmd README.md

_pkgdown.yml

codecov.yml

cran-comments.md

data-raw/.gitignore

data-raw/.replace_function_names.sh

data-raw/CreateTestObjects.R data-raw/Fig1.pdf

data-raw/Fig1.tex

data-raw/Fig1Simplified.Rmd

data-raw/Fig1Simplified.tex

data-raw/Fig3.Rmd

data-raw/Fig3TableModels.tex

data-raw/TestsForListCladePartitions.R

data-raw/TreeMGPMExample.tex

data-raw/TreeMGPMSimplified.tex

data/PCMBaseTestObjects.rda

data/dataFig3.rda

docs/404.html

docs/articles/Fig1.pdf

docs/articles/PCMBase.html

docs/articles/PCMBase_files/figure-html/unnamed-chunk-10-1.png

docs/articles/PCMBase_files/figure-html/unnamed-chunk-14-1.png

docs/articles/PCMBase_files/figure-html/unnamed-chunk-8-1.png

docs/articles/PCMBase_files/figure-html/unnamed-chunk-9-1.png

docs/articles/PCMCreateModel.html

docs/articles/PCMCreateModel_files/figure-html/unnamed-chunk-9-1.png

docs/articles/PCMParam.html

docs/articles/PCMTracePruning.html

docs/articles/index.html

docs/authors.html

docs/docsearch.css

docs/docsearch.js

docs/favicon.ico

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Args_MixedGaussian_MGPMDefaultModelTypes.html

docs/reference/Args_MixedGaussian_MGPMScalarOUType.html

docs/reference/Args_MixedGaussian_MGPMSurfaceOUType.html

docs/reference/FormatCellAsLatex.html

docs/reference/FormatTableAsLatex.html

docs/reference/MGPM.html

docs/reference/MGPMContext.html

docs/reference/MGPMPosK.html

docs/reference/MGPMScalarOUType.html

docs/reference/MGPMSurfaceOUType.html

docs/reference/MGPMVector.html

docs/reference/MatchListMembers.html

docs/reference/MixedGaussian.html

docs/reference/MixedGaussianTemplate.html

docs/reference/PCM.html

docs/reference/PCMAbCdEf.html

docs/reference/PCMAddToListAttribute.html

docs/reference/PCMApplyTransformation.html

docs/reference/PCMBaseIsADevRelease.html

docs/reference/PCMBaseTestObjects.html

docs/reference/PCMColorPalette.html

docs/reference/PCMCombineListAttribute.html

docs/reference/PCMCond.GaussianPCM.html

docs/reference/PCMCond.html

docs/reference/PCMCondVOU.html

docs/reference/PCMCreateLikelihood.html

docs/reference/PCMDefaultModelTypes.html

docs/reference/PCMDefaultObject.html

docs/reference/PCMDescribe.html

docs/reference/PCMDescribeParameters.html

docs/reference/PCMExtractDimensions.html

docs/reference/PCMExtractRegimes.html

docs/reference/PCMFindMethod.html

docs/reference/PCMFixParameter.html

docs/reference/PCMGenerateModelTypes.html

docs/reference/PCMGenerateParameterizations.html

docs/reference/PCMGetAttribute.html

docs/reference/PCMGetVecParamsRegimesAndModels.html

docs/reference/PCMInfo.html

docs/reference/PCMLik.html

docs/reference/PCMLikDmvNorm.html

docs/reference/PCMLikTrace.html

docs/reference/PCMListMembers.html

docs/reference/PCMListParameterizations.html

docs/reference/PCMLmr.html

docs/reference/PCMMapModelTypesToRegimes.html

docs/reference/PCMMean.html

docs/reference/PCMMeanAtTime.html

docs/reference/PCMModelTypes.html

docs/reference/PCMModels.html

docs/reference/PCMNumRegimes.html

docs/reference/PCMNumTraits.html

docs/reference/PCMOptions.html

docs/reference/PCMPExpxMeanExp.html

docs/reference/PCMPLambdaP_1.html

docs/reference/PCMPairSums.html

docs/reference/PCMParam.html

docs/reference/PCMParamCount.html

docs/reference/PCMParamGetShortVector.html

docs/reference/PCMParamLoadOrStore.html

docs/reference/PCMParamLocateInShortVector.html

docs/reference/PCMParamLowerLimit.html

docs/reference/PCMParamRandomVecParams.html

docs/reference/PCMParamSetByName.html

docs/reference/PCMParamType.html

docs/reference/PCMParamUpperLimit.html

docs/reference/PCMParentClasses.html

docs/reference/PCMParseErrorMessage.html

docs/reference/PCMPlotGaussianDensityGrid2D.html

docs/reference/PCMPlotGaussianSample2D.html

docs/reference/PCMPlotMath.html

docs/reference/PCMPlotTraitData2D.html

docs/reference/PCMPresentCoordinates.html

docs/reference/PCMRegimes.html

docs/reference/PCMSetAttribute.html

docs/reference/PCMSim.html

docs/reference/PCMSpecify.html

docs/reference/PCMTable.html

docs/reference/PCMTableParameterizations.html

docs/reference/PCMTrajectory-1.png

docs/reference/PCMTrajectory-2.png

docs/reference/PCMTrajectory.html

docs/reference/PCMTree-1.png

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docs/reference/PCMTree.html

docs/reference/PCMTreeBackbonePartition-1.png

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docs/reference/PCMTreeBackbonePartition.html

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docs/reference/PCMTreeDropClade.html

docs/reference/PCMTreeDtNodeParts.html

docs/reference/PCMTreeDtNodeRegimes.html

docs/reference/PCMTreeDtNodes.html

docs/reference/PCMTreeEdgeTimes.html

docs/reference/PCMTreeEvalNestedEDxOnTree-1.png

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docs/reference/PCMTreeEvalNestedEDxOnTree.html

docs/reference/PCMTreeExtractBackboneRegimes.html

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docs/reference/PCMTreeExtractClade.html

docs/reference/PCMTreeGetBranchLength.html

docs/reference/PCMTreeGetDaughters.html

docs/reference/PCMTreeGetLabels.html

docs/reference/PCMTreeGetParent.html

docs/reference/PCMTreeGetPartNames.html

docs/reference/PCMTreeGetPartRegimes.html

docs/reference/PCMTreeGetPartition.html

docs/reference/PCMTreeGetPartsForNodes.html

docs/reference/PCMTreeGetRegimeForNode.html

docs/reference/PCMTreeGetRegimesForEdges.html

docs/reference/PCMTreeGetRegimesForNodes.html

docs/reference/PCMTreeGetStartingNodesRegimes.html

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docs/reference/PCMTreeInsertSingletons.html

docs/reference/PCMTreeJumps.html

docs/reference/PCMTreeListAllPartitions-1.png

docs/reference/PCMTreeListAllPartitions.html

docs/reference/PCMTreeListCladePartitions.html

docs/reference/PCMTreeListDescendants.html

docs/reference/PCMTreeListRootPaths.html

docs/reference/PCMTreeLocateEpochOnBranches.html

docs/reference/PCMTreeLocateMidpointsOnBranches.html

docs/reference/PCMTreeMatchLabels.html

docs/reference/PCMTreeMatchRegimesWithModel.html

docs/reference/PCMTreeMatrixNodesInSamePart.html

docs/reference/PCMTreeMatrixNodesInSameRegime.html

docs/reference/PCMTreeMatrixTipsInSameRegime.html

docs/reference/PCMTreeNearestNodesToEpoch.html

docs/reference/PCMTreeNodeTimes.html

docs/reference/PCMTreeNumNodes.html

docs/reference/PCMTreeNumParts.html

docs/reference/PCMTreeNumTips.html

docs/reference/PCMTreeNumUniqueRegimes.html

docs/reference/PCMTreePlot.html

docs/reference/PCMTreePostorder.html

docs/reference/PCMTreePreorder.html

docs/reference/PCMTreeSetDefaultRegime.html

docs/reference/PCMTreeSetLabels.html

docs/reference/PCMTreeSetPartRegimes-1.png

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docs/reference/PCMTreeSetPartRegimes.html

docs/reference/PCMTreeSetPartition-1.png

docs/reference/PCMTreeSetPartition-2.png

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docs/reference/PCMTreeSetPartition.html

docs/reference/PCMTreeSetRegimes.html

docs/reference/PCMTreeSetRegimesForEdges-1.png

docs/reference/PCMTreeSetRegimesForEdges.html

docs/reference/PCMTreeSplitAtNode-1.png

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docs/reference/PCMTreeSplitAtNode.html

docs/reference/PCMTreeTableAncestors.html

docs/reference/PCMTreeToString.html

docs/reference/PCMTreeUniqueRegimes.html

docs/reference/PCMTreeVCV.html

docs/reference/PCMUnfixParameter.html

docs/reference/PCMVar.html

docs/reference/PCMVarAtTime.html

docs/reference/TruePositiveRate.html

docs/reference/UpperChol.html

docs/reference/UpperTriFactor.html

docs/reference/White.html

docs/reference/as.MGPM.html

docs/reference/as.MGPMVector.html

docs/reference/as.MixedGaussian.html

docs/reference/dataFig3.html

docs/reference/index.html

docs/reference/is.GaussianPCM.html

docs/reference/is.MGPM.html

docs/reference/is.MGPMContext.html

docs/reference/is.MGPMVector.html

docs/reference/is.MixedGaussian.html

docs/reference/is.PCM.html

docs/reference/is.PCMTree.html

docs/sitemap.xml

inst/CITATION

man/Args_MixedGaussian_MGPMDefaultModelTypes.Rd man/Args_MixedGaussian_MGPMScalarOUType.Rd man/Args_MixedGaussian_MGPMSurfaceOUType.Rd man/FormatCellAsLatex.Rd man/FormatTableAsLatex.Rd man/MGPMScalarOUType.Rd man/MGPMSurfaceOUType.Rd man/MatchListMembers.Rd man/MixedGaussian.Rd man/MixedGaussianTemplate.Rd man/PCM.Rd man/PCMAbCdEf.Rd man/PCMAddToListAttribute.Rd man/PCMApplyTransformation.Rd man/PCMBaseIsADevRelease.Rd man/PCMBaseTestObjects.Rd man/PCMColorPalette.Rd man/PCMCombineListAttribute.Rd man/PCMCond.GaussianPCM.Rd man/PCMCond.Rd man/PCMCondVOU.Rd man/PCMCreateLikelihood.Rd man/PCMDefaultModelTypes.Rd man/PCMDefaultObject.Rd man/PCMDescribe.Rd man/PCMDescribeParameters.Rd man/PCMExtractDimensions.Rd man/PCMExtractRegimes.Rd man/PCMFindMethod.Rd man/PCMFixParameter.Rd man/PCMGenerateModelTypes.Rd man/PCMGenerateParameterizations.Rd man/PCMGetAttribute.Rd man/PCMGetVecParamsRegimesAndModels.Rd man/PCMInfo.Rd man/PCMLik.Rd man/PCMLikDmvNorm.Rd man/PCMLikTrace.Rd man/PCMListMembers.Rd man/PCMListParameterizations.Rd man/PCMLmr.Rd man/PCMMapModelTypesToRegimes.Rd man/PCMMean.Rd man/PCMMeanAtTime.Rd man/PCMModelTypes.Rd man/PCMModels.Rd man/PCMNumRegimes.Rd man/PCMNumTraits.Rd man/PCMOptions.Rd man/PCMPExpxMeanExp.Rd man/PCMPLambdaP_1.Rd man/PCMPairSums.Rd man/PCMParam.Rd man/PCMParamCount.Rd man/PCMParamGetShortVector.Rd man/PCMParamLoadOrStore.Rd man/PCMParamLocateInShortVector.Rd man/PCMParamLowerLimit.Rd man/PCMParamRandomVecParams.Rd man/PCMParamSetByName.Rd man/PCMParamType.Rd man/PCMParamUpperLimit.Rd man/PCMParentClasses.Rd man/PCMParseErrorMessage.Rd man/PCMPlotGaussianDensityGrid2D.Rd man/PCMPlotGaussianSample2D.Rd man/PCMPlotMath.Rd man/PCMPlotTraitData2D.Rd man/PCMPresentCoordinates.Rd man/PCMRegimes.Rd man/PCMSetAttribute.Rd man/PCMSim.Rd man/PCMSpecify.Rd man/PCMTable.Rd man/PCMTableParameterizations.Rd man/PCMTrajectory.Rd man/PCMTree.Rd man/PCMTreeBackbonePartition.Rd man/PCMTreeDropClade.Rd man/PCMTreeDtNodes.Rd man/PCMTreeEdgeTimes.Rd man/PCMTreeEvalNestedEDxOnTree.Rd man/PCMTreeExtractClade.Rd man/PCMTreeGetBranchLength.Rd man/PCMTreeGetDaughters.Rd man/PCMTreeGetLabels.Rd man/PCMTreeGetParent.Rd man/PCMTreeGetPartNames.Rd man/PCMTreeGetPartRegimes.Rd man/PCMTreeGetPartition.Rd man/PCMTreeGetPartsForNodes.Rd man/PCMTreeGetRegimesForEdges.Rd man/PCMTreeGetRegimesForNodes.Rd man/PCMTreeGetTipsInPart.Rd man/PCMTreeGetTipsInRegime.Rd man/PCMTreeInsertSingletons.Rd man/PCMTreeJumps.Rd man/PCMTreeListAllPartitions.Rd man/PCMTreeListCladePartitions.Rd man/PCMTreeListDescendants.Rd man/PCMTreeListRootPaths.Rd man/PCMTreeLocateEpochOnBranches.Rd man/PCMTreeLocateMidpointsOnBranches.Rd man/PCMTreeMatchLabels.Rd man/PCMTreeMatrixNodesInSamePart.Rd man/PCMTreeNearestNodesToEpoch.Rd man/PCMTreeNodeTimes.Rd man/PCMTreeNumNodes.Rd man/PCMTreeNumParts.Rd man/PCMTreeNumTips.Rd man/PCMTreePlot.Rd man/PCMTreePostorder.Rd man/PCMTreePreorder.Rd man/PCMTreeSetLabels.Rd man/PCMTreeSetPartRegimes.Rd man/PCMTreeSetPartition.Rd man/PCMTreeSetRegimesForEdges.Rd man/PCMTreeSplitAtNode.Rd man/PCMTreeTableAncestors.Rd man/PCMTreeToString.Rd man/PCMTreeVCV.Rd man/PCMUnfixParameter.Rd man/PCMVar.Rd man/PCMVarAtTime.Rd man/RequireSuggestedPackages.Rd man/TruePositiveRate.Rd man/UpperTriFactor.Rd man/White.Rd man/as.MixedGaussian.Rd man/dataFig3.Rd man/is.GaussianPCM.Rd man/is.MixedGaussian.Rd man/is.PCM.Rd man/is.PCMTree.Rd tests/PosteriorQuantileTests/BM/BayesValidateBM.R

tests/PosteriorQuantileTests/BM/BayesValidateBM.RData

tests/PosteriorQuantileTests/BM/bsub.sh

tests/PosteriorQuantileTests/DOU/BayesValidateDOU.R

tests/PosteriorQuantileTests/DOU/BayesValidateDOU.RData

tests/PosteriorQuantileTests/DOU/Tree.RData

tests/PosteriorQuantileTests/DOU/bsub.sh

tests/PosteriorQuantileTests/DOU/lsf.o57137962

tests/PosteriorQuantileTests/ExplorePCMModelParams.Rmd tests/PosteriorQuantileTests/JOU/BayesValidateJOU.R

tests/PosteriorQuantileTests/JOU/BayesValidateJOU.RData

tests/PosteriorQuantileTests/JOU/Tree.RData

tests/PosteriorQuantileTests/JOU/bsub.sh

tests/PosteriorQuantileTests/JOU/lsf.o57226328

tests/PosteriorQuantileTests/JOU/lsf.o57245593

tests/PosteriorQuantileTests/OU/BayesValidateOU.R

tests/PosteriorQuantileTests/OU/BayesValidateOU.RData

tests/PosteriorQuantileTests/OU/bsub.sh

tests/PosteriorQuantileTests/PosteriorQuantileAnalysis.Rmd tests/PosteriorQuantileTests/PosteriorQuantileAnalysis.pdf tests/PosteriorQuantileTests/PosteriorQuantileCommon.R

tests/PosteriorQuantileTests/README

tests/PosteriorQuantileTests/old/JOU/GenSaveTree.R tests/PosteriorQuantileTests/old/JOU/postQuantileTools.R tests/PosteriorQuantileTests/old/JOU/runReplication.R tests/PosteriorQuantileTests/old/TwoSpeedOU/PosteriorQuantilesTwoSpeedOU.R tests/PosteriorQuantileTests/old/TwoSpeedOU/postQuantileTools.R tests/PosteriorQuantileTests/old/TwoSpeedOU/runReplication.R

tests/README.txt

tests/benchmark/testExpm.R tests/testthat.R

tests/testthat/.gitignore

tests/testthat/test-MixedGaussian.R tests/testthat/test-PCM.R tests/testthat/test-PCMLik-BM.R tests/testthat/test-PCMLik-BMdrift.R tests/testthat/test-PCMLik-DOU.R tests/testthat/test-PCMLik-OU.R tests/testthat/test-PCMParam.R tests/testthat/test-PCMSim.R tests/testthat/test-PCMTree.R tests/testthat/test-Transformations.R

vignettes/.gitignore

vignettes/Fig1.pdf vignettes/PCMBase.Rmd vignettes/PCMCreateModel.Rmd vignettes/PCMParam.Rmd vignettes/PCMTracePruning.Rmd

vignettes/REFERENCES-R.bib

vignettes/REFERENCES.bib

venelin/PCMBase documentation built on March 14, 2024, 8:24 p.m.